Abstract 4332: Characterizing cancer-associated fibroblasts in prostate cancer using Vizgen’s MERSCOPETM Platform
Authors: Ben Patterson, Cheng-Yi Chen, Nicolas Fernandez, Simran Kaushal, Leiam Colbert, Jiang He
Journal: Cancer Research (2023)

Abstract Understanding the spatial complexities within cancer provides crucial information for evaluating individual tumor development and progression; recent research in prostate cancer has shown how critical it is for oncologists to maintain a spatial context while characterizing a highly heterogeneous tumor microenvironment. As more and more research groups acknowledge the need for spatial biology solutions to solve difficult questions surrounding cell identity, heterogeneity, and interaction, Vizgen’s MERSCOPETM Platform provides a powerful tool to illuminate spatial information. Built on Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH) technology, Vizgen’s MERSCOPETM enables the direct profiling of the spatial organization of intact tissue with subcellular resolution. Here, we use a 500-gene panel to demonstrate the MERSCOPE’s spatial capability, assessing the canonical signaling pathways of cancer, cancer type-specific genes, select immune genes, proto-oncogenes, and tumor-suppressor genes in patient-derived prostate cancer samples. Using the Vizgen Cell Boundary Stain kit, we were able to generate a molecular and cellular atlas of these individual patient tumors by clustering cells based on gene expression and mapping these clusters back onto a spatial representation of the tumor. We found specific clusters relating to prognostic outcomes in cancer-associated fibroblasts (CAFs) and myofibroblasts. Subsequently, we used single-cell RNA-seq datasets to impute related transcriptome data for these various fibroblast clusters to help characterize them more specifically. To understand the heterogeneity intrinsic to CAFs, we performed a neighborhood analysis to determine how proximity to immune cells, tumor cells, and other stromal cells altered gene expression in different CAF clusters. We found gene expression changes associated with inflammation and reactive stromal signaling in CAFs based on their proximity to tumor versus stromal tissue compartments. We also compared the gene expression of tumor cells near CAFs to those more deeply embedded within the tumor compartment. This revealed interesting transcriptional covariations between superficial layers of tumor and their surrounding stromal milieu involved in cell proliferation and signaling. These analyses demonstrate the transcriptional variation possible across fibroblastic stromal cells acting in tumor-adjacent or stromal contexts. Notably, we were able to map and catalogue different patterns of gene expression relating to inflammation, tumor proliferation, and reactive stromal signaling. These findings demonstrate how the MERSCOPE platform can provide deep insights into the complex heterogeneity observed in the tumor microenvironment. Citation Format: Ben Patterson, Cheng-Yi Chen, Nicolas Fernandez, Simran Kaushal, Leiam Colbert, Jiang He. Characterizing cancer-associated fibroblasts in prostate cancer using Vizgen’s MERSCOPETM Platform. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4332.